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https://www.arca.fiocruz.br/handle/icict/25675
LEISHDB: A DATABASE OF CODING GENE ANNOTATION AND NON-CODING RNAS IN LEISHMANIA BRAZILIENSIS
Author
Affilliation
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Estadual de Feira de Santana. P os-Graduação em Computação Aplicada. Feira de Santana, BA, Brasil
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, Brasil
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile / Beagle Bioinformatics. Santiago, Chile / Instituto Vandique. João Pessoa, PB, Brasil
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Estadual de Feira de Santana. P os-Graduação em Computação Aplicada. Feira de Santana, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, Brasil
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, Brasil
Universidad Mayor. Facultad de Ciencias Centro de Genomica y Bioinformatica. Santiago, Chile / Beagle Bioinformatics. Santiago, Chile / Instituto Vandique. João Pessoa, PB, Brasil
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Estadual de Feira de Santana. P os-Graduação em Computação Aplicada. Feira de Santana, BA, Brasil / Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia. São Paulo, SP, Brasil
Abstract
Leishmania braziliensis is the etiological agent of cutaneous leishmaniasis, a disease
with high public health importance, affecting 12 million people worldwide. Although its
genome sequence was originally published in 2007, the two reference public annotations
still presents at least 80% of the genes simply classified as hypothetical or putative proteins.
Furthermore, it is notable the absence of non-coding RNA (ncRNA) sequences
from Leishmania species in public databases. These poorly annotated coding genes and
ncRNAs could be important players for the understanding of this protozoan biology, the
mechanisms behind host-parasite interactions and disease control. Herein, we performed
a new prediction and annotation of L. braziliensis protein-coding genes and noncoding
RNAs, using recently developed predictive algorithms and updated databases. In
summary, we identified 11 491 ORFs, with 5263 (45.80%) of them associated with proteins
available in public databases. Moreover, we identified for the first time the repertoire
of 11 243 ncRNAs belonging to different classes distributed along the genome. The
accuracy of our predictions was verified by transcriptional evidence using RNA-seq, confirming
that they are actually generating real transcripts. These data were organized in a
public repository named LeishDB (www.leishdb.com), which represents an improvement
on the publicly available data related to genomic annotation for L. braziliensis. This
updated information can be useful for future genomics, transcriptomics and metabolomics
studies; being an additional tool for genome annotation pipelines and novel studies
associated with the understanding of this protozoan genome complexity, organization biology, and development of innovative methodologies for disease control and
diagnostics.
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